I have a CM 690II case which has room to mount a 240mmx120mm radiator (I have the H100) on either the top or bottom. The tubes won't quite reach the CPU without putting some pressure on the GPU card if you run them from the bottom mounted radiator. I could be persuaded to invest in a pair of either Scythe Ultra Kaze 120x120x38mm or Sanyo Denki San Ace fans which at 38mm instead of 25mm would probably be able to reach the CPU without too much pressure on the GPU card.
Option 1.) I have been told that you want cool air to blow into the radiator...which would mean that if you installed it at the top you'd only have 1 exhaust fan total in the case (out the back) and be blowing the exhausted warm air from the radiator onto the MOBO area...as well as heat rising back into the radiator area. This setup doesn't seem ideal to me.
Option 2.) If you again install at the top of the case, but this time with the radiator fans pulling warm air from the MOBO/CPU area pushing it through the radiator out the top of the case...you are passing warm air through the radiator instead of cool air. This seems like a better option than option 1 though.
Option 3.) Getting either the Sanyo Denki or Scythe Ultra Kaze 120x120x38mm fans to mount the radiator on them at the bottom of the case having them draw cool air in and push it through the radiator. You would then be blowing in warm air from the radiator into the case/GPU area.
Option 4.) You could mount on the bottom with the stock fans pushing cool air from the front/bottom of the case through the radiator and have the Sanyo/Scythe (have to have these fans on bottom in order for the tubes to reach the CPU) pulling through the radiator and exhausting the warm air out the bottom of the case. The only "bad" thing about this way is that I would end up with the 3 exhaust fans at the top and back plus the 2 from the radiator and only 3 intake (1 from front and 2 from side)...not sure how bad that would be...maybe I could up the rpms on the intake fans?
Any of your options really are fine. The biggest thing you will run into is tubing length on the cooler, so your bottom mount option might not be feasible...but you'd have to see. When it comes to radiators, coolest air is always ideal. However, the air exiting the radiator isn't going to be that 'warm', so don't let airflow direction really be a big hang-up. The reason liquid cooling and better yet, real watercooling work so well is due to the much larger thermal capacity that water-based coolants have over air. They have the ability to absorb and transfer more heat, more quickly from a heat source which is why this kind of cooling excels when given adequate flow and radiator space for the heat source being cooled.
If your case already has good airflow, you shouldn't be worried about which way the fans on your rad are moving air or worry that the air will be anything more than lukewarm at most.
I'd personally place it where the air flow is naturally going (naturally meaning where the case fans direct the air), as more efficient air flow = more air flow with more fans = more cooling ability. Option 2 sounds the best to me in this regard.
The worst thing you could do is fight the air flow, which will create dead spots and make things hotter.